Yes, malnutrition can limit growth. This is a problem for people with eating disorders. The body can't build anything with materials it doesn't have.
In third world countries were a child has no option to eat enough, yea. If you were healthy in the first few years then it won't change a thing. There are many cases of anorexia were the person started with starving with 11 or so and still grows up to be tall (height = / = size or weight). One case I know of is a 6'3 guy who started with starving at age 13. The resorption of nutrients (inheridet metabolism) is far more important. As well as HGH.
Also if you really eat less the body takes its nutrients via other ways (breaks down its teeth for calcium etc.). But yet again, metabolism is doing it's thing without you thinking about it.
"You stunt your growth" is a foul excuse for people that just inheridet short genes honestly, the only real growth stunts are maybe accidents near growth plates, chemotherapy, maybe drug abuse (some drugs like retaline), or thyroid/kidney (or other organs) dysfunction. All things that the average person doesn't have to deal with.